package org.cbioportal.legacy.web;

import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf;

import com.fasterxml.jackson.databind.ObjectMapper;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.List;
import org.cbioportal.legacy.model.CopyNumberSeg;
import org.cbioportal.legacy.model.meta.BaseMeta;
import org.cbioportal.legacy.service.CopyNumberSegmentService;
import org.cbioportal.legacy.web.config.TestConfig;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.cbioportal.legacy.web.parameter.SampleIdentifier;
import org.hamcrest.Matchers;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
import org.springframework.boot.test.mock.mockito.MockBean;
import org.springframework.http.MediaType;
import org.springframework.security.test.context.support.WithMockUser;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.MockMvc;
import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
import org.springframework.test.web.servlet.result.MockMvcResultMatchers;
import org.springframework.web.context.WebApplicationContext;

@RunWith(SpringJUnit4ClassRunner.class)
@WebMvcTest
@ContextConfiguration(classes = {CopyNumberSegmentController.class, TestConfig.class})
public class CopyNumberSegmentControllerTest {

  private static final int TEST_SAMPLE_ID_1 = 1;
  private static final String TEST_SAMPLE_STABLE_ID_1 = "test_sample_stable_id_1";
  private static final int TEST_CANCER_STUDY_ID_1 = 1;
  private static final String TEST_CANCER_STUDY_IDENTIFIER_1 = "test_study_1";
  private static final Long TEST_SEG_ID_1 = 1L;
  private static final String TEST_CHR_1 = "test_chr_1";
  private static final Integer TEST_START_1 = 15;
  private static final Integer TEST_END_1 = 20;
  private static final Integer TEST_NUM_PROBES_1 = 3;
  private static final BigDecimal TEST_SEGMENT_MEAN_1 = new BigDecimal(0.2);
  private static final int TEST_SAMPLE_ID_2 = 2;
  private static final String TEST_SAMPLE_STABLE_ID_2 = "test_sample_stable_id_2";
  private static final int TEST_CANCER_STUDY_ID_2 = 2;
  private static final String TEST_CANCER_STUDY_IDENTIFIER_2 = "test_study_2";
  private static final Long TEST_SEG_ID_2 = 2L;
  private static final String TEST_CHR_2 = "test_chr_2";
  private static final Integer TEST_START_2 = 25;
  private static final Integer TEST_END_2 = 34;
  private static final Integer TEST_NUM_PROBES_2 = 5;
  private static final BigDecimal TEST_SEGMENT_MEAN_2 = new BigDecimal(0.4);

  private WebApplicationContext wac;

  @MockBean private CopyNumberSegmentService copyNumberSegmentService;

  private ObjectMapper objectMapper = new ObjectMapper();

  @Autowired private MockMvc mockMvc;

  @Test
  @WithMockUser
  public void getCopyNumberSegmentsInSampleInStudyDefaultProjection() throws Exception {

    List<CopyNumberSeg> copyNumberSegList = createExampleCopyNumberSegs();

    Mockito.when(
            copyNumberSegmentService.getCopyNumberSegmentsInSampleInStudy(
                Mockito.any(),
                Mockito.any(),
                Mockito.any(),
                Mockito.any(),
                Mockito.any(),
                Mockito.any(),
                Mockito.any(),
                Mockito.any()))
        .thenReturn(copyNumberSegList);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/studies/test_study_id/samples/test_sample_id/copy-number-segments")
                .accept(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].segId").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].studyId").value(TEST_CANCER_STUDY_IDENTIFIER_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].chromosome").value(TEST_CHR_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].start").value(TEST_START_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].end").value(TEST_END_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].numberOfProbes").value(TEST_NUM_PROBES_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].segmentMean").value(TEST_SEGMENT_MEAN_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].segId").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].studyId").value(TEST_CANCER_STUDY_IDENTIFIER_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].chromosome").value(TEST_CHR_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].start").value(TEST_START_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].end").value(TEST_END_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].numberOfProbes").value(TEST_NUM_PROBES_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].segmentMean").value(TEST_SEGMENT_MEAN_2));
  }

  @Test
  @WithMockUser
  public void getCopyNumberSegmentsInSampleInStudyMetaProjection() throws Exception {

    BaseMeta baseMeta = new BaseMeta();
    baseMeta.setTotalCount(2);

    Mockito.when(
            copyNumberSegmentService.getMetaCopyNumberSegmentsInSampleInStudy(
                Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(baseMeta);

    mockMvc
        .perform(
            MockMvcRequestBuilders.get(
                    "/api/studies/test_study_id/samples/test_sample_id/copy-number-segments")
                .param("projection", "META"))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(MockMvcResultMatchers.header().string(HeaderKeyConstants.TOTAL_COUNT, "2"));
  }

  @Test
  @WithMockUser
  public void fetchCopyNumberSegmentsDefaultProjection() throws Exception {

    List<CopyNumberSeg> copyNumberSegList = createExampleCopyNumberSegs();

    Mockito.when(
            copyNumberSegmentService.fetchCopyNumberSegments(
                Mockito.any(), Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(copyNumberSegList);

    List<SampleIdentifier> sampleIdentifiers = new ArrayList<>();
    SampleIdentifier sampleIdentifier1 = new SampleIdentifier();
    sampleIdentifier1.setStudyId(TEST_CANCER_STUDY_IDENTIFIER_1);
    sampleIdentifier1.setSampleId(TEST_SAMPLE_STABLE_ID_1);
    sampleIdentifiers.add(sampleIdentifier1);
    SampleIdentifier sampleIdentifier2 = new SampleIdentifier();
    sampleIdentifier2.setStudyId(TEST_CANCER_STUDY_IDENTIFIER_1);
    sampleIdentifier2.setSampleId(TEST_SAMPLE_STABLE_ID_2);
    sampleIdentifiers.add(sampleIdentifier2);

    mockMvc
        .perform(
            MockMvcRequestBuilders.post("/api/copy-number-segments/fetch")
                .with(csrf())
                .accept(MediaType.APPLICATION_JSON)
                .contentType(MediaType.APPLICATION_JSON)
                .content(objectMapper.writeValueAsString(sampleIdentifiers)))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(
            MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
        .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2)))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].segId").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[0].studyId").value(TEST_CANCER_STUDY_IDENTIFIER_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].chromosome").value(TEST_CHR_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].start").value(TEST_START_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].end").value(TEST_END_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].numberOfProbes").value(TEST_NUM_PROBES_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[0].segmentMean").value(TEST_SEGMENT_MEAN_1))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].segId").doesNotExist())
        .andExpect(
            MockMvcResultMatchers.jsonPath("$[1].studyId").value(TEST_CANCER_STUDY_IDENTIFIER_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].sampleId").value(TEST_SAMPLE_STABLE_ID_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].chromosome").value(TEST_CHR_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].start").value(TEST_START_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].end").value(TEST_END_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].numberOfProbes").value(TEST_NUM_PROBES_2))
        .andExpect(MockMvcResultMatchers.jsonPath("$[1].segmentMean").value(TEST_SEGMENT_MEAN_2));
  }

  @Test
  @WithMockUser
  public void fetchCopyNumberSegmentsMetaProjection() throws Exception {

    BaseMeta baseMeta = new BaseMeta();
    baseMeta.setTotalCount(2);

    Mockito.when(
            copyNumberSegmentService.fetchMetaCopyNumberSegments(
                Mockito.any(), Mockito.any(), Mockito.any()))
        .thenReturn(baseMeta);

    List<SampleIdentifier> sampleIdentifiers = new ArrayList<>();
    SampleIdentifier sampleIdentifier1 = new SampleIdentifier();
    sampleIdentifier1.setStudyId(TEST_CANCER_STUDY_IDENTIFIER_1);
    sampleIdentifier1.setSampleId(TEST_SAMPLE_STABLE_ID_1);
    sampleIdentifiers.add(sampleIdentifier1);
    SampleIdentifier sampleIdentifier2 = new SampleIdentifier();
    sampleIdentifier2.setStudyId(TEST_CANCER_STUDY_IDENTIFIER_1);
    sampleIdentifier2.setSampleId(TEST_SAMPLE_STABLE_ID_2);
    sampleIdentifiers.add(sampleIdentifier2);

    mockMvc
        .perform(
            MockMvcRequestBuilders.post("/api/copy-number-segments/fetch")
                .with(csrf())
                .param("projection", "META")
                .contentType(MediaType.APPLICATION_JSON)
                .content(objectMapper.writeValueAsString(sampleIdentifiers)))
        .andExpect(MockMvcResultMatchers.status().isOk())
        .andExpect(MockMvcResultMatchers.header().string(HeaderKeyConstants.TOTAL_COUNT, "2"));
  }

  private List<CopyNumberSeg> createExampleCopyNumberSegs() {
    List<CopyNumberSeg> copyNumberSegList = new ArrayList<>();
    CopyNumberSeg copyNumberSeg1 = new CopyNumberSeg();
    copyNumberSeg1.setSegId(TEST_SEG_ID_1);
    copyNumberSeg1.setCancerStudyId(TEST_CANCER_STUDY_ID_1);
    copyNumberSeg1.setCancerStudyIdentifier(TEST_CANCER_STUDY_IDENTIFIER_1);
    copyNumberSeg1.setSampleId(TEST_SAMPLE_ID_1);
    copyNumberSeg1.setSampleStableId(TEST_SAMPLE_STABLE_ID_1);
    copyNumberSeg1.setChr(TEST_CHR_1);
    copyNumberSeg1.setStart(TEST_START_1);
    copyNumberSeg1.setEnd(TEST_END_1);
    copyNumberSeg1.setNumProbes(TEST_NUM_PROBES_1);
    copyNumberSeg1.setSegmentMean(TEST_SEGMENT_MEAN_1);
    copyNumberSegList.add(copyNumberSeg1);
    CopyNumberSeg copyNumberSeg2 = new CopyNumberSeg();
    copyNumberSeg2.setSegId(TEST_SEG_ID_2);
    copyNumberSeg2.setCancerStudyId(TEST_CANCER_STUDY_ID_2);
    copyNumberSeg2.setCancerStudyIdentifier(TEST_CANCER_STUDY_IDENTIFIER_2);
    copyNumberSeg2.setSampleId(TEST_SAMPLE_ID_2);
    copyNumberSeg2.setSampleStableId(TEST_SAMPLE_STABLE_ID_2);
    copyNumberSeg2.setChr(TEST_CHR_2);
    copyNumberSeg2.setStart(TEST_START_2);
    copyNumberSeg2.setEnd(TEST_END_2);
    copyNumberSeg2.setNumProbes(TEST_NUM_PROBES_2);
    copyNumberSeg2.setSegmentMean(TEST_SEGMENT_MEAN_2);
    copyNumberSegList.add(copyNumberSeg2);
    return copyNumberSegList;
  }
}
